miRNA: 3'- aCGU-UGUGGUGa---------GGGCCACAGUUG-CC- -5'
miRNA: 3'- aCGuuGuGGUG-AG-GGCCACAGUUGCc -5'
miRNA: 3'- -ACG-----UUGUGGUGAGGG--CCACA-----GUugCC- -5'
miRNA: 3'- -ACGUUGUGGUGAGGGCCACAGUUGCC- -5'
Results 1 - 4 of 4 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. | strand | Start Position | R_P_ratio# |
P value
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| Predicted miRNA align pattern | |||||||
| 15549 | 3' | -54.1 | NC_004004.1 | + | 2379 | 0.67 | 0.220812 |
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Target: 5'- gGCAcACAUCACcgugcccuacCUCGGUGUCAACaGGu -3' miRNA: 3'- aCGU-UGUGGUGa---------GGGCCACAGUUG-CC- -5' |
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| 15549 | 3' | -54.1 | NC_004004.1 | + | 6650 | 0.67 | 0.201382 |
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Target: 5'- cGCucCuCCACaUCuCUGGUGUCGACGa -3' miRNA: 3'- aCGuuGuGGUG-AG-GGCCACAGUUGCc -5' |
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| 15549 | 3' | -54.1 | NC_004004.1 | + | 6210 | 0.68 | 0.195243 |
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Target: 5'- aUGCucucaGACGCCGCUCUCauGGUGUugcacCGugGGa -3' miRNA: 3'- -ACG-----UUGUGGUGAGGG--CCACA-----GUugCC- -5' |
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| 15549 | 3' | -54.1 | NC_004004.1 | + | 433 | 1.12 | 0.000055 |
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Target: 5'- uUGCAACACCACUCCCGGUGUCAACGGg -3' miRNA: 3'- -ACGUUGUGGUGAGGGCCACAGUUGCC- -5' |
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Note:
When operating RNAhybrid, the pipeline first calculates the perfect minimum free energy (Perfect mfe *) of a putative miRNA when the entire putative miRNA binds to a perfectly complementary target site, then it calculates the minimum free energy of RNA duplex (mfe of the miRNA/mRNA duplex), abbreviated as Rd_mfe. An alignment for which the Rd_mfe to its correspondent Perfect mfe ratio (R_P_ratio #) is more than 66% is regarded as a positive alignment as described by Krek et al. (21). The P_value is calculated by RNAhybrid.
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